Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53704.51 
• Atom Count: 3784 
• Residue Count: 494 
• Unique protein chains: 1

2YPI

CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS

• DOI: 10.2210/pdb2YPI/pdb

• Classification: TRIOSE PHOSPHATE ISOMERASE
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


• Deposited: 1990-01-12 Released: 1991-01-15 
• Deposition Author(s): Lolis, E., Petsko, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å

Literature

Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis.

Lolis, E., Petsko, G.A.

(1990) Biochemistry 29: 6619-6625

• PubMed: 2204418 


• PubMed Abstract: 
  

The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a final R factor of 0.18. The interactions between the inhibitor and enzyme have been analyzed. The inhibitor forms hydrogen bonds to the side chains of His 95 and Glu 165. The latter hydrogen bond confirms that Glu 165 is protonated upon PGA binding. The structure of the complexed enzyme has been compared to that of the unbound form of the enzyme, and conformational changes have been observed: the side chain of Glu 165 moves over 2 A and a 10-residue flexible loop moves over 7 A to close over the active site. Spectroscopic results of phosphoglycolic acid binding to triosephosphate isomerase that have been amassed over the years are also explained in structural terms. The implications for catalysis are noted.

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Related Citations: 

• Structure of Yeast Triosephosphate Isomerase at 1.9-Angstroms Resolution
  Lolis, E.,Alber, T.,Davenport, R.C.,Rose, D.,Hartman, F.C.,Petsko, G.A.
  (1990) Biochemistry 29: 6609
• Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark)
  Alber, T.C.,Davenportjunior, R.C.,Giammona, D.A.,Lolis, E.,Petsko, G.A.,Ringe, D.
  (1987) Cold Spring Harbor Symp.Quant.Biol. 52: 603
• On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
  Alber, T.,Banner, D.W.,Bloomer, A.C.,Petsko, G.A.,Phillips, D.,Rivers, P.S.,Wilson, I.A.
  (1981) Philos.Trans.R.Soc.London,Ser.B 293: 159
• Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
  Alber, T.,Hartman, F.C.,Johnson, R.M.,Petsko, G.A.,Tsernoglou, D.
  (1981) J.Biol.Chem. 256: 1356




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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRIOSEPHOSPHATE ISOMERASE	A, B	247	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: TPI1 EC: 5.3.1.1
Find proteins for P00942 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: TPI1 Go to UniProtKB:  P00942

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PGA	A, B	2-PHOSPHOGLYCOLIC ACID C2 H5 O6 P ASCFNMCAHFUBCO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PGA	Ki: 15000 nM BINDINGMOAD
PGA	Ki: 15000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.350	α = 90.00
b = 83.970	β = 99.70
c = 38.670	γ = 90.00

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1990-01-12 
• Released Date: 1991-01-15 
• Deposition Author(s): Lolis, E., Petsko, G.A.

Revision History 

• Version 1.0: 1991-01-15
  Type: Initial release
• Version 1.1: 2008-03-25
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance